sps_tissue
Example data for `MetCirc`: `sps_tissue`
Bundled with MetCirc · exported, loads via data()
Class
–
Missing
–
Format
rda · xz
version 3 · 20 KB
File
data/spectra.RData
Fingerprint
–
Format documented
Yes
Source
data("idMSMStissueproject", package = "MetCirc") ## get all MS/MS spectra tissue <- tissue[tissue[, "id"] id_uniq <- unique(tissue[, "id"]) ## obtain precursor m/z from id_uniq prec_mz <- lapply(strsplit(as.character(id_uniq), split = "_"), "[", 1) |> unlist() |> as.numeric() ## obtain m/z from fragments per precursor m/z mz_l <- lapply(id_uniq, function(id_i) tissue[tissue[, "id"] == id_i, "mz"]) ## obtain corresponding intensity values int_l <- lapply(id_uniq, function(id_i) tissue[tissue[, "id"] == id_i, "intensity"]) ## order mz and intensity values int_l <- lapply(seq_along(int_l), function(i) int_l[[i]][order(mz_l[[i]])]) mz_l <- lapply(seq_along(mz_l), function(i) sort(mz_l[[i]])) ## obtain retention time by averaging all retention time values rt <- lapply(id_uniq, function(id_i) tissue[tissue[, "id"] == id_i, "rt"]) |> lapply(mean) |> unlist() ## create list of Spectra objects and concatenate sps_l <- lapply(seq_len(length(mz_l)), function(i) spd <- S4Vectors::DataFrame( name = as.character(i), rtime = rt[i], msLevel = 2L, precursorMz = prec_mz[i]) spd$mz <- list(mz_l[[i]]) spd$intensity <- list(int_l[[i]]) Spectra::Spectra(spd)) sps_tissue <- Reduce(c, sps_l) ## combine list of spectrum2 objects to MSpectra object, ## use SPL, LIM, ANT, STY for further analysis sps_tissue@metadata <- data.frame( compartmentTissue[, c("SPL", "LIM", "ANT", "STY")]) save(sps_tissue, file = "spectra.RData", compress = "xz")
Columns
Nothing inside this object was measured, so there is no column list, no counts and no fingerprint to compare it with. The file holds an S4 object this reader can name and not open, so none of its slots were reached. What is recorded is the file it lives in and which releases carry it.
Version history
| Version | Released | Size | Change | Stored as | Confidence |
|---|---|---|---|---|---|
| 3.23 | 2026-04-28 | – | Not compared | rda · xz version 3 · 20 KB | degraded |
| 3.22 | 2025-10-29 | – | Not compared | rda · xz version 3 · 20 KB | degraded |
| 3.21 | 2025-04-15 | – | Not compared | rda · xz version 3 · 20 KB | degraded |
| 3.20 | 2024-10-29 | – | Not compared | rda · xz version 3 · 20 KB | degraded |
| 3.19 | 2024-04-30 | – | Not compared | rda · xz version 3 · 20 KB | degraded |
| 3.18 | 2023-10-24 | – | Not compared | rda · xz version 3 · 20 KB | degraded |
| 3.17 | 2023-04-25 | – | Not compared | rda · xz version 3 · 20 KB | degraded |
| 3.16 | 2022-11-01 | – | – | rda · xz version 3 · 20 KB | degraded |